Does your IR system have any kind of RF link. Some systems pick up the remote and then relay it wirelessly to the repeater. If that's the case, it could be something at night creating RF interference.

I'll assume no RF is involved - answer a few questions for us.

Are you having this problem with both the stb and the sony receiver or just the stb?

If it's just the stb, try moving the emitter around while in the failure mode to locate a position where it will work. If it's both the stb and the sony, chances are, the failure is occurring before the signal gets to the emitters, so the flashing repeater light might not be indicative of a good signal - only that it's getting one. Have you tried turning off the light when in failure mode to see if that helps? Some CFLs can cause interference, and it might be greater at night when there's less ambient light. Let us know on these points.